Rodrigo Borgia and "Take Your Grandson to Work Day": He's watching baby Giovanni while Lucrezia rests, and brings the fussing child into a meeting with the entire College of Cardinals and the French ambassador. He sits upon the Papal throne, still bouncing and hushing the baby, and hisses "Pianissimo!" at the ambassador for being too loud.
And tells the baby to ignore the "nasty Ambasssador."
And in the scene just before:
Cardinal Sforza: The French Ambassador awaits, your Holiness.
In the same scene he's lamenting the fact that he's given up "intimacy" for lent. His expression is excellent, as is Vannozza telling him that he can leave - meaning that he can no longer ogle her while she's having a bath.
Honestly, her cackle - which verges on Evil Laugh - is just the capper. She's having such fun messing with Rodrigo. Not to mention her roundabout mention of their "water being cold".
In the same scene he engages in a great bit of Self-Deprecation about his own ugliness when he says "and as you can see, with these looks, I have no vanity". He also calls them out with "so, God is reduced to breaking windows", with such biting sarcasm that even the kids get it. The way the kid keeps trying to play the tough guy by mindlessly reciting what Savanarola told him would also be quite funny, if he didn't have the potential to do serious harm.
Upon returning to Rome, Juan gives Rodrigo a box of cigars as a gift which the Holy Father initially believes are “turds.” An increasingly irritated Juan then suffers to instruct him on how to smoke one, despite his father’s almost childlike reactions. Hilarity Ensues.
Rodrigo: “Ahh! We are on fire!”
Rodrigo’s bouts of flustered incoherence. Most recently, when an exasperated Vannozza tells him that why she’s been put in charge of handling an unruly Lucrezia’s marriage arrangements is “a mystery” to her, his reply is:
As well as the fact that sarcastic, well-spoken Rodrigo is completely unable to articulate his anger due to the fact that Vannozza is holding the baby. Vannozza's raised eyebrow and fierce glare say it all - "stop bellowing around the children!"
Alfonso of Aragon's morphing expression as Cesare and Lucrezia dance in "The Confession". It changes from bemused to jealous to "oh god what have I married into?".
Also, Cesare misinterpreting Lucrezia's "Marry me" and spinning a tale of them running away to a fishing village and changing their names. Sure, it's completely crazy and kind of weird—but it's also completely Cesare. Probably because it's crazy and weird.
It speaks volumes about the show and its fans that the line "I have long suspected my brother of having congress with my angelic sister" brings reactions of "SO HAVE WE" and... incoherent laughter.
Cesare dragging Juan out of bed in a whorehouse and dunking his head in a bucket of water.
Any time Micheletto is holding baby Giovanni in the season 3 opener. Just the visual of badass Micheletto, scary beard and armor, holding a baby in a lacy dress. The best part is near the end when a fussy Giovanni is handed off to Micheletto and instantly stops crying. Babies love assassins!
In the same episode, there is something darkly amusing in the scene where Della Rovere enters the room. Rovere's Oh Crap must be seen to be believed:
Della Rovere: My brothers, I came as soon as I heard.
In the same episode, Cardinal Sforza goes to the assassin his family sent and proclaims Rodrigo's survival: "When I left he was calling for water, by now he's probably fucking some servant girl with a wine jug in one hand and a swan's leg in the other". The best part is he just sounds irritated (either by Rodrigo's survival or by his family's scheming,) but not in the least bit surprised by either one.
Cesare's reaction upon finding a naked Lucrezia waiting for him in her bed. Seeing the show's cold as iceMagnificent Bastard tongue-tied and stammering is enough to send anyone into tears of laughter.
Rodrigo gives a Rousing Speech about the necessity of a "crusade" against the Turks who are damaging Venice's trade, and as soon as everyone is cheering he hands out reams of new taxes and levies.
Pope Alexander has some good moments of this in "Relics". There's his opening scene, in which The Cardinals are so afraid of him that they wait for him to sit down so they can sit as well, but he keeps rising from his chair and they're forced to do the same. Three times.. Then he tries to conduct a business conversation with Ascanio as he takes care of his bees, much to Ascanio's exasperation ("Taste the honey of Rome, Cardinal!"). And finally, as he is being sold the [supposed] Spear of Longinuis by a Jew, he picks up The [supposed] Spear Of Longinus, a priceless christian artifact, and almost breaks over his knee, causing the jew to briefly flip his shit in the most hilarious manner possible.
The escalating relic war between Rome and the Sforzas (the Pope produces the Spear of Longinus, so Caterina makes the shroud of Constantinople and fakes a miracle,) Cesare openly laughs at how ridiculous it's getting.
Rodrigo is presented with Giulia Farnese's new soon-to-be husband and is asked for approval. Hilarity Ensues.
Vincenzo Salvatore: My tool is the feather's crow, your holiness, I plow with that.